+++ /dev/null
-<HTML>
-<HEAD>
-<TITLE>g_dih</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
-Thu 26 Aug 2010</B></td></tr></TABLE>
-<HR>
-<H3>Description</H3>
-<p>
-g_dih can do two things. The default is to analyze dihedral transitions
-by merely computing all the dihedral angles defined in your topology
-for the whole trajectory. When a dihedral flips over to another minimum
-an angle/time plot is made.<p>
-The opther option is to discretize the dihedral space into a number of
-bins, and group each conformation in dihedral space in the
-appropriate bin. The output is then given as a number of dihedral
-conformations sorted according to occupancy.
-<P>
-<H3>Files</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> hello.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
-</TABLE>
-<P>
-<H3>Other options</H3>
-<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
-<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print version info and quit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sa</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Perform cluster analysis in dihedral space instead of analysing dihedral transitions. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-mult</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> mulitiplicity for dihedral angles (by default read from topology) </TD></TD>
-</TABLE>
-<P>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
-</div>
-</BODY>
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <gmx_ana.h>
-
-
-/* This is just a wrapper binary.
-* The code that used to be in g_dih.c is now in gmx_dih.c,
-* where the old main function is called gmx_dih().
-*/
-int
-main(int argc, char *argv[])
-{
- gmx_dih(argc,argv);
- return 0;
-}
-
-
-
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
- * Copyright (c) 2012, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
-
-#include "sysstuff.h"
-#include "string2.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "smalloc.h"
-#include "statutil.h"
-#include "nrama.h"
-#include "physics.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "vec.h"
-#include "gmx_ana.h"
-
-
-#define NOMIN 'X'
-
-static void ana_dih(FILE *out,char *index,int nframes,real dih[],t_dih *dd)
-{
- int i;
- real mind,maxd,sum,av,var,prev,width;
- gmx_bool bTrans;
-
- mind=5400,maxd=-5400,sum=0,av=0,var=0;
-
- prev=dih[0];
- for(i=0; (i<nframes); i++) {
- if ((dih[i]-prev) > 180) {
- /* PBC.. */
- dih[i]-=360;
- }
- else if ((dih[i]-prev) < -180)
- dih[i]+=360;
- prev=dih[i];
-
- sum+=dih[i];
- mind=min(mind,dih[i]);
- maxd=max(maxd,dih[i]);
- }
- av=sum/nframes;
- for(i=0; (i<nframes); i++)
- var+=sqr(dih[i]-av);
- var/=nframes;
- width=(360.0/dd->mult);
- bTrans=((maxd - mind) > width);
-
- fprintf(out,"%-10s %10.3f %10.3f %10.3f %10.3f %10.3f %-10s%3.0f\n",
- index,mind,av,maxd,var,sqrt(var),
- bTrans ? "Yep" : "",width);
-}
-
-static int find_min(real phi,int ntab,real phitab[])
-{
- int i,imin;
- real mind,mm;
- real width;
-
- /* Set closest minimum to the first one */
- width=360.0/ntab;
- mind=fabs(phi-phitab[0]);
- imin=0;
- for(i=1; (i<ntab); i++) {
- mm=fabs(phi-phitab[i]);
- if (mm < mind) {
- imin=i;
- mind=mm;
- }
- }
- if (mind < width*0.5 )
- return imin;
- else
- return -1;
-}
-
-static int vphi(t_dih *dih,real phi,int mult)
-{
- static real m2[] = { 90, 270 };
- static real m3[] = { 60, 180, 300 };
- static real m4[] = { 45, 135, 225, 315 };
- static real m6[] = { 30, 90, 150, 210, 270, 330 };
-
- real phiref;
- int vpp=0;
-
- phiref=RAD2DEG*(phi-dih->phi0);
- while (phiref < 0)
- phiref+=360;
- while (phiref > 360)
- phiref-=360;
-
- switch(mult) {
- case 2:
- vpp=find_min(phiref,2,m2);
- break;
- case 3:
- vpp=find_min(phiref,3,m3);
- break;
- case 4:
- vpp=find_min(phiref,4,m4);
- break;
- case 6:
- vpp=find_min(phiref,6,m6);
- break;
- default:
- gmx_fatal(FARGS,"No such multiplicity %d",dih->mult);
- }
-
- if (vpp == -1)
- return NOMIN;
- else
- return vpp+'0';
-}
-
-typedef struct t_cluster {
- int ndih;
- int freq;
- char *minimum;
- struct t_cluster *next;
-} t_cluster;
-
-static t_cluster *search_cluster(t_cluster *cl,char *minimum)
-{
- t_cluster *ccl=cl;
-
- while (ccl != NULL) {
- if (strcmp(minimum,ccl->minimum)==0)
- return ccl;
- ccl=ccl->next;
- }
- return NULL;
-}
-
-static void add_cluster(t_cluster **cl,int ndih,char *minimum)
-{
- t_cluster *loper;
- t_cluster *ccl;
-
- snew(ccl,1);
- ccl->ndih=ndih;
- ccl->freq=1;
- ccl->minimum=strdup(minimum);
- ccl->next=NULL;
-
- if (*cl == NULL)
- *cl=ccl;
- else {
- loper=*cl;
- while (loper->next != NULL)
- loper=loper->next;
- loper->next=ccl;
- }
-}
-
-static void p_cluster(FILE *out,t_cluster *cl)
-{
- t_cluster *loper;
-
- fprintf(out,"* * * C L U S T E R A N A L Y S I S * * *\n\n");
- fprintf(out," Frequency Dihedral minima\n");
- loper=cl;
- while (loper != NULL) {
- fprintf(out,"%10d %s\n",loper->freq,loper->minimum);
- loper=loper->next;
- }
-}
-
-static void ana_cluster(FILE *out, t_xrama *xr,real **dih,real time[],
- t_topology *top,int nframes,int mult)
-{
- t_cluster *cl=NULL,*scl;
- char *minimum;
- int i,j,nx;
-
- /* Number of dihedrals + terminating NULL
- * this allows for using string routines
- */
- snew(minimum,xr->ndih+1);
-
- for(i=0; (i<nframes); i++) {
- nx=0;
- for(j=0; (j<xr->ndih); j++) {
- minimum[j] = vphi(&xr->dih[j],dih[j][i],
- mult == -1 ? xr->dih[j].mult : mult);
- if (minimum[j] == NOMIN)
- nx++;
- }
- if (nx == 0) {
- if ((scl=search_cluster(cl,minimum)) == NULL)
- add_cluster(&cl,xr->ndih,minimum);
- else
- scl->freq++;
- }
- }
- p_cluster(out,cl);
-
- sfree(minimum);
-}
-
-static void ana_trans(FILE *out, t_xrama *xr,real **dih,real time[],
- t_topology *top,int nframes, const output_env_t oenv)
-{
- FILE *outd;
- real prev_phi,prev_psi;
- int i,j,phi,psi;
- char buf[10];
-
- fprintf(out,"\n\t* * * D I H E D R A L S T A T I S T I C S * * *\n\n");
- fprintf(out,"%-10s %10s %10s %10s %10s %10s %10s\n",
- "index","minimum","average","maximum","variance","std.dev",
- "transition");
- for(i=0; (i<xr->ndih); i++) {
- sprintf(buf,"dih-%d",i);
- ana_dih(out,buf,nframes,dih[i],&(xr->dih[i]));
- }
- for(i=0; (i<xr->npp); i++) {
- sprintf(buf,"%s",xr->pp[i].label);
- outd=xvgropen(buf,"Dihedral Angles","Time (ps)","Degrees",oenv);
-
- phi=xr->pp[i].iphi;
- psi=xr->pp[i].ipsi;
- prev_phi=dih[phi][0];
- prev_psi=dih[psi][0];
- for(j=0; (j<nframes); j++) {
- /* PBC.. */
- if ((dih[phi][j]-prev_phi) > 180)
- dih[phi][j]-=360;
- else if ((dih[phi][j]-prev_phi) < -180)
- dih[phi][j]+=360;
- prev_phi=dih[phi][j];
- if ((dih[psi][j]-prev_psi) > 180)
- dih[psi][j]-=360;
- else if ((dih[psi][j]-prev_psi) < -180)
- dih[psi][j]+=360;
- prev_psi=dih[psi][j];
- fprintf(outd,"%10g %10g %10g\n",time[j],prev_phi,prev_psi);
- }
- ffclose(outd);
- }
-}
-
-int gmx_dih(int argc,char *argv[])
-{
- const char *desc[] = {
- "[TT]g_dih[tt] can do two things. The default is to analyze dihedral transitions",
- "by merely computing all the dihedral angles defined in your topology",
- "for the whole trajectory. When a dihedral flips over to another minimum",
- "an angle/time plot is made.[PAR]",
- "The opther option is to discretize the dihedral space into a number of",
- "bins, and group each conformation in dihedral space in the",
- "appropriate bin. The output is then given as a number of dihedral",
- "conformations sorted according to occupancy."
- };
- static int mult = -1;
- static gmx_bool bSA = FALSE;
- t_pargs pa[] = {
- { "-sa", FALSE, etBOOL, {&bSA},
- "Perform cluster analysis in dihedral space instead of analysing dihedral transitions." },
- { "-mult", FALSE, etINT, {&mult},
- "mulitiplicity for dihedral angles (by default read from topology)" }
- };
- FILE *out;
- t_xrama *xr;
- t_topology *top;
- real **dih,*time;
- real dd;
- int i,nframes,maxframes=1000;
- output_env_t oenv;
- t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
- { efOUT, NULL, NULL, ffWRITE }
- };
-#define NFILE asize(fnm)
-
- CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
-
- if (mult != -1)
- fprintf(stderr,"Using %d for dihedral multiplicity rather than topology values\n",mult);
-
- snew(xr,1);
- init_rama(oenv,ftp2fn(efTRX,NFILE,fnm),
- ftp2fn(efTPX,NFILE,fnm),xr,3);
- top=read_top(ftp2fn(efTPX,NFILE,fnm),NULL);
-
- /* Brute force malloc, may be too big... */
- snew(dih,xr->ndih);
- for(i=0; (i<xr->ndih); i++)
- snew(dih[i],maxframes);
- snew(time,maxframes);
-
- fprintf(stderr,"\n");
- nframes = 0;
- while (new_data(xr)) {
- for(i=0; (i<xr->ndih); i++) {
- dd=xr->dih[i].ang*RAD2DEG;
- while (dd < 0)
- dd+=360;
- while (dd > 360)
- dd-=360;
- dih[i][nframes]=dd;
- }
- time[nframes]=xr->t;
- nframes++;
- if (nframes > maxframes) {
- maxframes += 1000;
- for(i=0; (i<xr->ndih); i++)
- srenew(dih[i],maxframes);
- srenew(time,maxframes);
- }
- }
-
- fprintf(stderr,"\nCalculated all dihedrals, now analysing...\n");
-
- out=ftp2FILE(efOUT,NFILE,fnm,"w");
-
- if (bSA) {
- /* Cluster and structure analysis */
- ana_cluster(out,xr,dih,time,top,nframes,mult);
- }
- else {
- /* Analyse transitions... */
- ana_trans(out,xr,dih,time,top,nframes,oenv);
- }
- ffclose(out);
-
- thanx(stderr);
-
- return 0;
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff